Direct Detection of Carbapenem-Resistant Organisms from Environmental Samples Using the GeneXpert Molecular Diagnostic System

mSphere. 2018 Aug 1;3(4):e00113-18. doi: 10.1128/mSphere.00113-18.


In this pilot study, traditional culture and PCR methods were compared to the Cepheid GeneXpert IV molecular diagnostic system with the Xpert Carba-R assay (Carba-R assay) for detection of carbapenem resistance genes in primary environmental samples collected during a health care-related outbreak. Overall, traditional culture-dependent PCR and the Carba-R assay demonstrated 75% agreement. The Carba-R assay detected carbapenemase genes in five additional samples and in two samples that had additional genes when compared to culture-dependent PCR. The Carba-R assay could be useful for prioritizing further testing of environmental samples during health care-related outbreaks.IMPORTANCE Use of the Carba-R assay for detection of carbapenem-resistant Gram-negative organisms (CROs) can provide data for implementation of a rapid infection control response to minimize the spread of CROs in the health care setting.

Keywords: Cepheid GeneXpert; PCR; carbapenem resistant; carbapenemase genes.

Publication types

  • Comparative Study
  • Evaluation Study

MeSH terms

  • Anti-Bacterial Agents / pharmacology*
  • Bacteriological Techniques / methods
  • Carbapenems / pharmacology*
  • Environmental Microbiology*
  • Gram-Negative Bacteria / drug effects*
  • Gram-Negative Bacteria / genetics
  • Gram-Negative Bacteria / isolation & purification*
  • Molecular Diagnostic Techniques / methods*
  • Pilot Projects
  • Polymerase Chain Reaction / methods
  • beta-Lactam Resistance*


  • Anti-Bacterial Agents
  • Carbapenems